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The net file format is used to describe the axtNet data that underlie the net alignment annotations in the Genome Browser. For a detailed description of the methods used to generate these data, refer to the Genome Browser description pages that accompany the Net alignment tracks.
File format
The net file consists of 7 fixed fields and a set of optional name/value pairs. In the descriptions below, target refers to the reference species and query refers to the aligning species.
- Fixed fields:
- Class. Either fill or gap. Fill refers to a portion of a chain.
- Start in chromosome (target species)
- Size (target species)
- Chromsome name (query species)
- Relative orientation between target and query species.
- Start in chromsome (query species)
- Size (query species)
- Name/value pairs (optional):
- id -- ID of associated chain (gapped alignment), if any.
- score -- Score of associated chain.
- ali -- Number of bases in alignments in chain.
- qFar -- For fill that is on the same chromosome as parent, how far fill is from position predicted by parent. This helps determine if a rearrangement is local or if a duplication is tandem.
- qOver -- Number of bases overlapping with parent gap on query side. Generally, this will be near zero, except for inverts.
- qDup -- Number of bases in query region that are used twice or more in net. This helps distinguish between a rearrangement and a duplication.
- type -- One of the following values:
- top -- Chain is top-level, not a gap filler
- syn -- Chain is on same chromosome and in same direction as parent
- inv -- Chain is on same chromosome on opposite direction from parent
- nonSyn -- Chain is on a different chromosome from parent
- tN -- Number of unsequenced bases (Ns) on target side
- qN -- Number of unsequenced bases on query side
- tR -- Number of bases in RepeatMasker masked repeats on target.
- qR -- Number of bases in RepeatMasker masked repeats on query.
- tNewR -- Bases in lineage-specific repeats on target.
- qNewR -- Bases in lineage-specific repeats on query.
- tOldR -- Bases in repeats predating split on target.
- qOldR -- Bases in repeats predating split on query.
- tTrf -- Bases in trf (Tandem Repeat Finder) repeats on target.
- qTrf -- Bases in trf repeats on query.
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